NAME
Bio::Protease - Digest your protein substrates with customizable
specificity
VERSION
version 1.112980
SYNOPSIS
use Bio::Protease;
my $protease = Bio::Protease->new(specificity => 'trypsin');
my $protein = 'MRAERVIKP';
# Perform a full digestion
my @products = $protease->digest($protein);
# products: ( 'MR', 'AER', 'VIKP' )
# Get all the siscile bonds.
my @sites = $protease->cleavage_sites($protein);
# sites: ( 2, 5 )
# Try to cut at a specific position.
@products = $protease->cut($protein, 2);
# products: ( 'MR', 'AERVIKP' )
DESCRIPTION
This module models the hydrolitic behaviour of a proteolytic enzyme. Its
main purpose is to predict the outcome of hydrolitic cleavage of a
peptidic substrate.
The enzyme specificity is currently modeled for 37 enzymes/reagents.
This models are somewhat simplistic as they are largely regex-based, and
do not take into account subtleties such as kinetic/temperature effects,
accessible solvent area, secondary or tertiary structure elements.
However, the module is flexible enough to allow the inclusion of any of
these effects by consuming the module's interface, Bio::ProteaseI.
Alternatively, if your desired specificity can be correctly described by
a regular expression, you can pass it to the specificity attribute at
construction time. See specificity below.
ATTRIBUTES
specificity
Set the enzyme's specificity. Required. Could be either of:
* an enzyme name: e.g. 'enterokinase'
my $enzyme = Bio::Protease->new(specificity => 'enterokinase');
There are currently definitions for 37 enzymes/reagents. See
Specificities.
* a regular expression:
my $motif = qr/MN[ED]K[^P].{3}/,
my $enzyme = Bio::Protease->new( specificity => $motif );
The motif should always describe an 8-character long peptide. When a
an octapeptide matches the regex, its 4th peptidic bond (ie, between
the 4th and 5th letter) will be marked for cleaving or reporting.
For example, the peptide AMQRNLAW is recognized as follows:
.----..----.----..----. .-----.-----.-----.-----.
| A || M | Q || R |*| N | L | A | W |
|----||----|----||----|^|-----|-----|-----|-----|
| P4 || P3 | P2 || P1 ||| P1' | P2' | P3' | P4' |
'----''----'----''----'|'-----'-----'-----'-----'
cleavage site
Some specificity rules can only be described with more than one
regular expression (see the case for trypsin, for example). To
account for those cases, you can also pass an array reference of
regular expressions; all of which should match the given
octapeptide:
my $rule = [$rule1, $rule2, $rule3];
my $enzyme = Bio::Protease->new( specificity => $rule );
In the case your particular specificity rule requires an "or"
clause, you can use the "|" separator in a single regex.
Specificities
This class attribute contains a hash reference with all the available
regexep-based specificities. The keys are the specificity names, the
value is an arrayref with the regular expressions that define them.
my @protease_pool = do {
Bio::Protease->new(specificity => $_)
for keys %{Bio::Protease->Specificities};
}
As a rule, all specificity names are lower case. Currently, they
include:
* alcalase
* arg-cproteinase
* asp-n_endopeptidase
* asp-n_endopeptidase_glu
* bnps_skatole
* caspase_1
* caspase_2
* caspase_3
* caspase_4
* caspase_5
* caspase_6
* caspase_7
* caspase_8
* caspase_9
* caspase_10
* chymotrypsin
* chymotrypsin_low
* clostripain
* cnbr
* enterokinase
* factor_xa
* formic_acid
* glutamyl_endopeptidase
* granzymeb
* hydroxylamine
* iodosobenzoic_acid
* lysc
* lysn
* ntcb
* pepsin_ph1.3
* pepsin
* proline_endopeptidase
* proteinase_k
* staphylococcal_peptidase i
* thermolysin
* thrombin
* trypsin
For a complete description of their specificities, you can check out
,
or look at the regular expressions of their definitions in this same
file.
use_cache
Turn caching on, trading memory for speed. Defaults to 0 (no caching).
Useful when any method is being called several times with the same
argument.
my $p = Bio::Protease->new( specificity => 'trypsin', use_cache => 0 );
my $c = Bio::Protease->new( specificity => 'trypsin', use_cache => 1 );
my $substrate = 'MAAEELRKVIKPR' x 10;
$p->digest( $substrate ) for (1..1000); # time: 5.11s
$c->digest( $substrate ) for (1..1000); # time: 0.12s
cache
The cache object, which has to do the Cache::Ref::Role::API role. Uses
Cache::Ref::LRU by default with a cache size of 5000, but you can set
this to your liking at construction time:
my $p = Bio::Protease->new(
use_cache => 1,
cache => Cache::Ref::Random->new( size => 50 ),
specificity => 'trypsin'
);
METHODS
digest
Performs a complete digestion of the peptide argument, returning a list
with possible products. It does not do partial digests (see method "cut"
for that).
my @products = $enzyme->digest($protein);
cut
Attempt to cleave $peptide at the C-terminal end of the $i-th residue
(ie, at the right). If the bond is indeed cleavable (determined by the
enzyme's specificity), then a list with the two products of the
hydrolysis will be returned. Otherwise, returns false.
my @products = $enzyme->cut($peptide, $i);
cleavage_sites
Returns a list with siscile bonds (bonds susceptible to be cleaved as
determined by the enzyme's specificity). Bonds are numbered starting
from 1, from N to C-terminal. Takes a string with the protein sequence
as an argument:
my @sites = $enzyme->cleavage_sites($peptide);
is_substrate
Returns true or false whether the peptide argument is a substrate or
not. Esentially, it's equivalent to calling "cleavage_sites" in boolean
context, but with the difference that this method short-circuits when it
finds its first cleavable site. Thus, it's useful for CPU-intensive
tasks where the only information required is whether a polypeptide is a
substrate of a particular enzyme or not
SEE ALSO
* PeptideCutter
This module's idea is largely based on Expasy's PeptideCutter
(). For more information
on the experimental evidence that supports both the algorithm and
the specificity definitions, check their page.
AUTHOR
Bruno Vecchi
COPYRIGHT AND LICENSE
This software is copyright (c) 2011 by Bruno Vecchi.
This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.